Hi Todd,
Index pulses can be connected to any input and are detected by software in a C User Program in a similar manner as with a home switch. If the index pulse is a differential signal and you have a Kanalog board with available differential inputs then it would be best to use those. Typically the C program is written to Jog until the Home switch is detected, then Jog slower until the Index pulse is detected then stop. The index pulse must be longer than 180us long so that it can be detected by software. This usually isn't a problem.
IHTH
TK